pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

201818 citationsJournal Articlegold Open Access

Authors

Sven Warris · Wageningen University & Research

N. Roshan N. Timal · Delft University of Technology

Marcel Kempenaar · Hanze University of Applied Sciences

Arne M. Poortinga · Hanze University of Applied Sciences

Henri van de Geest · Wageningen University & Research

Ana Lucia Vărbănescu · Delft University of Technology

Jan‐Peter Nap

Abstract

pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.

Topics & Keywords

Genomics and Phylogenetic Studies Algorithms and Data Compression RNA modifications and cancer

Publication Details

Published in: PLoS ONE

Volume 13, Issue 1, pp. e0190279-e0190279

DOI: 10.1371/journal.pone.0190279

Field-Weighted Citation Impact: 1.11

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pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

Authors

Abstract

Topics & Keywords

Publication Details